[BioSQL-l] load_ncbi_taxonomy.pl error

[Seth Johnson]

Sorry, it didn't occur to me that running out of space was MySQL related. :)

On 9/13/06, aaron.j.mackey at gsk.com <aaron.j.mackey at gsk.com> wrote:
>
> strange or not, that is exactly what MySQL error 28 means: no space left
> on device.
>
> -Aaron
>
> "Seth Johnson" <johnson.biotech at gmail.com> wrote on 09/13/2006 01:43:45
> PM:
>
> > That would be strange since I've tried it on Sun Solaris and Windows
> > XP (with gigs of free space) with same exact results.
>
> > On 9/13/06, aaron.j.mackey at gsk.com <aaron.j.mackey at gsk.com> wrote:
> > Most likely you've run out of space in /var/tmp ...
> >
> > -Aaron
> >
> > biosql-l-bounces at lists.open-bio.org wrote on 09/13/2006 11:06:28 AM:
> >
> > > Hello,
> > > I'm a newbie to BioSQl, trying to set it up on mySQL server following
> > the
> > > installation directions and ran into a problem.  When trying to load
> the
> > > taxonomic info, I get an error at 230000+ line.  Progress dump
> follows.
> > > Have I missed anything???
> > > =======================================
> > > # perl load_ncbi_taxonomy.pl -dbname BioSQL_1 -host localhost -port
> 3306
> > > -dbuser root -dbpass xxxxx -verbose=2 -download
> > > Loading NCBI taxon database in taxdata:
> > >         ... retrieving all taxon nodes in the database
> > >         ... reading in taxon nodes from nodes.dmp
> > >         ... insert / update / delete taxon nodes
> > >                 10000/324120 done (in 15 secs, 666.7 rows/s)
> > >                 20000/324120 done (in 15 secs, 666.7 rows/s)
> > >                 30000/324120 done (in 15 secs, 666.7 rows/s)
> > >                 40000/324120 done (in 15 secs, 666.7 rows/s)
> > >                 50000/324120 done (in 15 secs, 666.7 rows/s)
> > >                 60000/324120 done (in 14 secs, 714.3 rows/s)
> > >                 70000/324120 done (in 15 secs, 666.7 rows/s)
> > >                 80000/324120 done (in 14 secs, 714.3 rows/s)
> > >                 90000/324120 done (in 15 secs, 666.7 rows/s)
> > >                 100000/324120 done (in 14 secs, 714.3 rows/s)
> > >                 110000/324120 done (in 16 secs, 625.0 rows/s)
> > >                 120000/324120 done (in 15 secs, 666.7 rows/s)
> > >                 130000/324120 done (in 14 secs, 714.3 rows/s)
> > >                 140000/324120 done (in 15 secs, 666.7 rows/s)
> > >                 150000/324120 done (in 15 secs, 666.7 rows/s)
> > >                 160000/324120 done (in 14 secs, 714.3 rows/s)
> > >                 170000/324120 done (in 14 secs, 714.3 rows/s)
> > >                 180000/324120 done (in 15 secs, 666.7 rows/s)
> > >                 190000/324120 done (in 15 secs, 666.7 rows/s)
> > >                 200000/324120 done (in 14 secs, 714.3 rows/s)
> > >                 210000/324120 done (in 15 secs, 666.7 rows/s)
> > >                 220000/324120 done (in 14 secs, 714.3 rows/s)
> > >                 230000/324120 done (in 15 secs, 666.7 rows/s)
> > > failed to insert node (281015;281015;3817;species;1;1): Error writing
> > file
> > > '/var/tmp/MLtydiOb' (Errcode: 28) at load_ncbi_taxonomy.pl line 545.
> > > #
> > > ===================================================
> > >
> > >
> > > --
> > > Best Regards,
> > >
> > >
> > > Seth Johnson
> > > Senior Bioinformatics Associate
> > >
> > > Ph: (202) 470-0900
> > > Fx: (775) 251-0358
> > > _______________________________________________
> > > BioSQL-l mailing list
> > > BioSQL-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/biosql-l
> > >
> >
>
> >
> >
> >
> > --
> > Best Regards,
> >
> >
> > Seth Johnson
> > Senior Bioinformatics Associate
> >
> > Ph: (202) 470-0900
> > Fx: (775) 251-0358
>
>


-- 
Best Regards,


Seth Johnson
Senior Bioinformatics Associate

Ph: (202) 470-0900
Fx: (775) 251-0358